Final PhyloCode Database, Representative Allele Sequences, and Intermediate Processing Reports

This dataset contains the final PhyloCode database and associated files generated during the construction of PhyloCode values for Escherichia coli cgMLST alleles. PhyloCode is a numerical representation of cgMLST allele identifiers based on phylogenetic relationships among alleles. Allele sequences from 2,513 E. coli cgMLST loci were processed by BLAST-based filtering, multiple sequence alignment, SNP-based allele grouping, phylogenetic tree reconstruction, patristic distance calculation, circular ordering, and normalization of cumulative distances to the interval [0, π]. The uploaded files include the final locus-specific PhyloCode database files, representative allele sequences, per-locus processing summaries, and intermediate processing reports generated during PhyloCode construction. These files support reproducibility of the PhyloCode database construction and can be used together with the PhyloCode source code and protocols.io workflow. The corresponding source code is available at:https://github.com/suzukimasahiro/PhyloCode/ The detailed workflow is available at protocols.io:https://doi.org/10.17504/protocols.io.5jyl8356dv2w/v1